[ccp4bb] structure determination from a hollow crystal

Dear all, Is there a documented case of a structure determination from a hollow crystal? We have the unfortunate situation that a protein only crystallizes as a hollow tube, where the inside is filled with solvent, which ruins the diffraction patterns. I was often confronted with similar situa

[ccp4bb] To win or not twinning?

Dear CCP4ers, I'd like to kindly ask your advice. Sorry for the long e-mail. I have crystals of a 12.3 KDa protein that grow in hexagon-like patterns, link for the crystal image: http://fullonline.org/science/cryst01.jpg XDS, Phenix and Pointless always suggest that the data sets for these

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

And again, has anyone seen the code to even know what's going on "under the hood"? Thanks, Steve > On Nov 29, 2016, at 8:35 PM, dusan turk wrote: > > Guys, > > I have a two issues to add here: > > 1. RSZS validation does not tolerate chain IDs longer than 1 character, > so it kills one of t

[ccp4bb] RapiData at SSRL 2017

There are two weeks left to apply for the RapiData 2017 course on Data Collection and Structure Solving. The course will take place at SSRL on April 16-21 2017. It is a great venue for young scientists to learn how to optimize macromolecular crystallography experiments at synchrotron beamlines a

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

Guys, I have a two issues to add here: 1. RSZS validation does not tolerate chain IDs longer than 1 character, so it kills one of the very essential reasons why mmCIF format was introduced (to enable deposition of large structures in a single file). 2. I have noticed in validation report of

[ccp4bb] ccp4 package manager

CCP4 package manager doesn't work for me when I try a fresh ccp4 installation. It goes through all the question dialogs, but then fails to download the actual installation package, complaining of broken network connection. Multiple tries don't help. Obviously, I can get around this by downloadin

Re: [ccp4bb] wavelet application in CCP4

Thanks for all you providing these info. Charles On Mon, Nov 28, 2016 at 4:33 PM, Alexandre OURJOUMTSEV wrote: > Dear Charles, > > > if you are interested in applications of wavelets to macromolecular > crystallography problems, you may look also at a slightly earlier > publication by Vladimir L

Re: [ccp4bb] Density for an unknown ligand

Benzopinacol? It's sometimes used as the initiator for radical polymerisations, so its presence in plasticware wouldn't be unheard of. On 2016-11-27 10:33, Wei Liu wrote: Dear all, We have recently crystallized a recombinant protein produce from E. coli, and determined the structure at 1.9 Å.

Re: [ccp4bb] Density for an unknown ligand

Wei, Did you crystallize your protein in plastic trays? If my memory serves me, there is at least one case of monoamine oxidase B (from the Edmondson and Mattevi groups) where MOAB bound the plasticizer from the wells. You might want to explore that direction as well. Regards, Michael

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

I started a ccp4 thread a few years ago about RSRZ score calculations favoring trimmed side chains because they produce better scores. Based on what I could find at that time, it looked like the density of your structure was compared to the density of that residue type in submitted PDBs of similar

Re: [ccp4bb] Calculation of RSRZ Score in PDB Validation Reports

Is the code publically available for the RSRZ calculation? Thanks, Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan Merritt Sent: Tuesday, November 29, 2016 12:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Calculation of RSRZ S

[ccp4bb] Postdoc position in structural microbiology at Newcastle University (UK)

Dear All, A position is available immediately for an enthusiastic and highly motivated Research Assistant/Associate in the laboratories of Prof Bert van den Berg and Dr David Bolam within the Institute for Cell & Molecular Biosciences at Newcastle University. The p

Re: [ccp4bb] Density for an unknown ligand

Hello Wei, There is a simple way of assessing the Biphenyl in your condition is as follows: 1) You can take you concentrated mother liquor (given: if you are sure no aromatic compound is available in ML) and take a absorption spectra at wavelength range of 200-300, if you get a maxima at near about

Re: [ccp4bb] Density for an unknown ligand

Dear Wei,to get more information on this putative “butterfly-like” ligand, you can perform non-denaturing and denaturing mass spectrometry. This should give you the molecular weight of this compound, which most probably comes from E. coli and co-purifies with your protein of interest. In parallel,